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Related Concept Videos

Protein-protein Interfaces02:04

Protein-protein Interfaces

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Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a...
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An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
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Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective. They may serve in transport, storage, or membranes; or they may be toxins or enzymes. Their structures, like their functions, vary greatly. They are all, however, amino acid polymers arranged in a linear sequence.
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Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
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Discovering Protein Interactions and Characterizing Protein Function Using HaloTag Technology
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Methods for Discovering and Targeting Druggable Protein-Protein Interfaces and Their Application to Repurposing.

E Sila Ozdemir1, Farideh Halakou2, Ruth Nussinov3,4

  • 1Department of Chemical and Biological Engineering, Koc University, Istanbul, Turkey.

Methods in Molecular Biology (Clifton, N.J.)
|December 15, 2018
PubMed
Summary

Drug repurposing identifies new uses for existing drugs by targeting protein-protein interactions (PPIs). This review explores strategies for predicting hot spots and binding pockets on PPI interfaces to improve drug discovery.

Keywords:
Hot regionsHot spotsInterface motifsNetwork-based approachesProtein interface clustering

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Area of Science:

  • Biochemistry
  • Pharmacology
  • Computational Biology

Background:

  • Drug repurposing accelerates therapeutic development by utilizing approved drugs for new indications.
  • Identifying novel protein targets for existing drugs remains a significant challenge in drug discovery.
  • Protein-protein interaction (PPI) networks offer a promising avenue for uncovering new drug targets.

Purpose of the Study:

  • To review protein-protein interaction (PPI) interface-targeting strategies for drug repurposing.
  • To highlight the importance of hot spot residue and hot region prediction in identifying drug targets.
  • To present common methods for identifying drug off-targets within PPI networks.

Main Methods:

  • Review of literature on PPI interface-targeting strategies for drug repurposing.
  • Discussion of hot spot residue and hot region prediction methods.
  • Illustration of PPI network analysis techniques for off-target identification.
  • Compilation of online resources for hot spot prediction, binding pocket identification, and interface clustering.

Main Results:

  • Protein interface analysis, including hot spot prediction, is crucial for effective drug repurposing.
  • Computational methods can identify potential drug off-targets within complex PPI networks.
  • Available online resources facilitate the prediction of key interaction sites and clustering of interfaces.
  • Case studies demonstrate the practical significance of targeting protein interfaces and hot spots.

Conclusions:

  • Targeting protein-protein interaction interfaces, particularly hot spots, is a viable strategy for drug repurposing.
  • Computational tools and online resources enhance the identification of new therapeutic applications for existing drugs.
  • Further improvements in PPI interface analysis will advance polypharmacology and drug discovery efforts.